Methylophilus luteus (DSM 22949, CCUG 58412, VKM B-2548)

Name: Methylophilus luteus (DSM 22949, CCUG 58412, VKM B-2548)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7243

Type strain

Strain Designation Mim

Culture col. no. DSM 22949 CCUG 58412 VKM B-2548 Mim

NCBI tax ID(s) 640108

Special Collections DSMZ CCUG Literature strains

History DSMZ <- Y. A. Trotsenko, Inst. Biochem. Physiol. Microorg., RAS, Pushchino, Russia; Mim <- N. V. Doronina

Links

Methylophilus luteus Mim is an aerobe, spore-forming, Gram-negative bacterium that was isolated from phyllosphere of coltsfoot Tussilago farfara L..

spore-forming Gram-negative rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 403749

VKM B-2548,VKM B-2547,DSM 22949,CCUG 58412,CCUG 58411T

@ref 20215

Last LPSN update 2026-05-29 08:26:36

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Spirillales

Family Methylophilaceae

Genus Methylophilus

Species Methylophilus luteus

Full scientific name Methylophilus luteus Gogleva et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
29722	negative	1.9-2 µm	0.2-0.3 µm	rod-shaped
125439	negative					99.375

Pigmentation

29722

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16627	MEDIUM K (DSMZ Medium 1122)		Medium recipe at MediaDive	Name: MEDIUM K (DSMZ Medium 1122) Composition: Agar 20.0 g/l KH2PO4 2.0 g/l (NH4)2SO4 2.0 g/l NaCl 0.5 g/l MgSO4 x 7 H2O 0.125 g/l FeSO4 x 7 H2O 0.002 g/l Methanol Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16627	positive	growth	28
29722	positive	growth	24-26
29722	positive	optimum	24-26

Culture pH

@ref	Ability	Type	PH
29722	positive	optimum	7.2-7.8
29722	positive	growth	7.2-7.8

Physiology and metabolism

Oxygen tolerance

29722

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
29722
125439		99.954

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29722	NaCl	positive	growth	0.05 %
29722	NaCl	positive	optimum	0.05 %

Observation

29722

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29722	29987 ChEBI	glutamate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29722	catalase	+	1.11.1.6
29722	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
16627	phyllosphere of coltsfoot Tussilago farfara L.	Tussilago farfara	Moscow, Pushchino	Russia	RUS	Europe

Taxonmaps

69479

Global distribution of 16S sequence FJ872109 (>99% sequence identity) for Methylophilus from Microbeatlas

Aquatic Samples	478
Soil Samples	122
Animal Samples	350
Plant Samples	330
Total Samples	1280

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16627	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM4267626v1 assembly for Methylophilus luteus CCUG 58412	scaffold	GCA_042676265	640108	68.97

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16627	Methylophilus luteus strain Mim 16S ribosomal RNA gene, partial sequence	FJ872109	1418		640108

GC content

@ref	GC-content (mol%)	Method
16627	54.5	thermal denaturation, midpoint method (Tm)
29722	54.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM4267626v1 assembly for Methylophilus luteus CCUG 58412
NCBI: GCA_042676265

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	89.71	no
125439	gram_stain	BacteriaNetⓘ	negative	99.38	no
125439	motility	BacteriaNetⓘ	yes	72.13	no
125439	spore_formation	BacteriaNetⓘ	no	99.95	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Clubroot-Induced Changes in the Root and Rhizosphere Microbiome of Susceptible and Resistant Canola.	Cordero-Elvia J, Galindo-Gonzalez L, Fredua-Agyeman R, Hwang SF, Strelkov SE.	Plants (Basel)	10.3390/plants13131880	2024
Metabolism	Isolation and genomic characterization of Novimethylophilus kurashikiensis gen. nov. sp. nov., a new lanthanide-dependent methylotrophic species of Methylophilaceae.	Lv H, Sahin N, Tani A.	Environ Microbiol	10.1111/1462-2920.14062	2018
Phylogeny	Methylophilus flavus sp. nov. and Methylophilus luteus sp. nov., aerobic, methylotrophic bacteria associated with plants.	Gogleva AA, Kaparullina EN, Doronina NV, Trotsenko YA	Int J Syst Evol Microbiol	10.1099/ijs.0.019455-0	2009

References

#16627	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22949
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#26105	IJSEM 2623 2010 ( DOI 10.1099/ijs.0.019455-0 , PubMed 20023062 )
#29722	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26105
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Methylophilus luteus (DSM 22949, CCUG 58412, VKM B-2548)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042676265

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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